Microbiome definition re-visited: old concepts and new challenges
Author
Berg, GabrieleRybakova, Daria
Fischer, Doreen
Cernava, Tomislav
Vergès, Marie-Christine C
Charles, Trevor
Chen, Xiaoyulong
Cocolin, Luca
Eversole, Kellye
Corral, Gema H
Kazou, Maria
Kinkel, Linda
Lange, Lene
Lima, Nelson
Loy, Alexander
Macklin, James A
Maguin, Emmanuelle
Mauchline, Tim
McClure, Ryan
Mitter, Birgit
Ryan, Matthew
Sarand, Inga
Smidt, Hauke
Schelkle, Bettina
Roume, Hugo
Kiran, G. S
Selvin, Joseph
Souza, Rafael S C d
van Overbeek, Leo
Singh, Brajesh K
Wagner, Michael
Walsh, Aaron M.
Sessitsch, Angela
Schloter, Michael
Keyword
MicrobiomeDate
2020-06-30
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Berg, G., Rybakova, D., Fischer, D. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103 (2020). https://doi.org/10.1186/s40168-020-00875-0Abstract
Abstract The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term “microbiome.” Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video AbstractFunder
European UnionGrant Number
818116ae974a485f413a2113503eed53cd6c53
https://doi.org/10.1186/s40168-020-00875-0